The majority of biochemical samples are complex mixtures. Separation and isolation of each component prior to analysis is often laborious and tedious. Therefore, considerable effort has been expended on the development and application of methodologies designed to separate and introduce each separated component of a mixture directly into a mass spectrometer. GC/MS, used for the separation and analysis of volatile and thermally stable substances is a relatively mature technique. LC/MS, which combines liquid chromatographic separation with MS analysis is still at a stage where several interfaces are in popular use and where the capabilities of the technique in its various manifestations have not been thoroughly explored. We are currently exploring the applicability of thermospray (TSP) as an LC-MS interface to biochemical problems. One project involves the use of LC/MS for the detection of methylated nucleosides in order to relate these DNA modifications to altered gene expression. TSP LC/MS was used to determine the background level of the modified nucleosides in untreated calf thymus and salmon sperm DNA. In this study we have identified several methylated guanosines. A second major area of current interest is the development of TSP LC/MS for the determination of glutathione conjugates of exogenous chemicals and the mercapturic acid metabolites. Our results indicate that the mercapturic acid metabolites and derivatized glutathione conjugates can be successfully analyzed by this technique.